System Identification

machine learning and neuroscience
system identification

Deep networks have set new standards for accurately predicting responses of neurons in visual cortex to arbitrary images. However, these models still do not account for all the explainable variability of the neuronal responses in primary visual cortex. We are building better models for the visual system of mice and monkeys that can accurately predict responses and their per trial variability as well as estimate the general state that the brain was in during presentation of arbitrary visual inputs.

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Lab members are shown in this color.

2025

Lisa Schmors, Dominic Gonschorek, Jan Niklas Böhm, Yongrong Qiu, Na Zhou, Dmitry Kobak, Andreas Tolias, Fabian H. Sinz, Jacob Reimer, Katrin Franke, Sebastian Damrich, Philipp Berens TRACE: Contrastive learning for multi-trial time-series data in neuroscience arXiv preprint · system identification · arXiv
Eric Y. Wang, Paul G. Fahey, Zhuokun Ding, Stelios Papadopoulos, Kayla Ponder, Marissa A. Weis, Andersen Chang, Taliah Muhammad, Saumil Patel, Zhiwei Ding, Dat Tran, Jiakun Fu, Casey M. Schneider-Mizell, R. Clay Reid, Forrest Collman, Nuno Maçarico da Costa, Katrin Franke, Alexander S. Ecker, Jacob Reimer, Xaq Pitkow, Fabian H. Sinz, Andreas S. Tolias Foundation model of neural activity predicts response to new stimulus types Nature journal paper · system identification · bioRxiv nature
Mohammad Bashiri¹, Luca Baroni¹, Jan Antolik, Fabian H. Sinz Learning and aligning single-neuron invariance manifolds in visual cortex ICLR (oral; <1.8% submissions; 34. overall; 1. neuroscience) , equal contribution: ¹ conference paper · system identification · OpenReview GitHub

2024

Finn Schmidt, Suhas Shrinivasan¹, Polina Turishcheva¹, Fabian Sinz Modeling dynamic neural activity by combining naturalistic video stimuli and stimulus-independent latent factors NeuReps @ NeurIPS 2024 , equal contribution: ¹ workshop paper · system identification · arXiv
Polina Turishcheva, Max Burg, Fabian H. Sinz, Alexander Ecker Reproducibility of predictive networks for mouse visual cortex NeurIPS conference paper · system identification · NeurIPS (spotlight) arXiv
Polina Turishcheva, Paul G. Fahey, Michaela Vystrčilová, Laura Hansel, Rachel E Froebe, Kayla Ponder, Yongrong Qiu, Konstantin Friedrich Willeke, Mohammad Bashiri, Ruslan Baikulov, Yu Zhu, Lei Ma, Shan Yu, Tiejun Huang, Bryan M. Li, Wolf De Wulf, Nina Kudryashova, Matthias H. Hennig, Nathalie Rochefort, Arno Onken, Eric Wang, Zhiwei Ding, Andreas S. Tolias, Fabian H. Sinz, Alexander S Ecker Retrospective for the Dynamic Sensorium Competition for predicting large-scale mouse primary visual cortex activity from videos NeurIPS 2024 conference paper · system identification · competition page OpenReview
Nan Wu, Isabel Valera, Fabian H. Sinz, Alexander Ecker, Thomas Euler, Yongrong Qiu Probabilistic Neural Transfer Function Estimation with Bayesian System Identification PLoS CB journal paper · system identification · arXiv PLoS CB
Taesung Jung, Nanyu Zeng, Jason D. Fabbri, Guy Eichler, Zhe Li, Konstantin Willeke, Katie E. Wingel, Agrita Dubey, Rizwan Huq, Mohit Sharma, Yaoxing Hu, Girish Ramakrishnan, Kevin Tien, Paolo Mantovani, Abhinav Parihar, Heyu Yin, Denise Oswalt, Alexander Misdorp, Ilke Uguz, Tori Shinn, Gabrielle J. Rodriguez, Cate Nealley, Ian Gonzales, Michael Roukes, Jeffrey Knecht, Daniel Yoshor, Peter Canoll, Eleonora Spinazzi, Luca P. Carloni, Bijan Pesaran, Saumil Patel, Brett Youngerman, R. James Cotton, Andreas Tolias, Kenneth L. Shepard Stable, chronic in-vivo recordings from a fully wireless subdural-contained 65,536-electrode brain-computer interface device bioRxiv preprint · system identification · bioRxiv
Mohammad Bashiri PhD Thesis, International Max Planck Research School for Intelligent Systems, Tübingen phd thesis · system identification · pdf

2023

Max F. Burg, Thomas Zenkel, Michaela Vystrčilová, Jonathan Oesterle, Larissa Höfling, Konstantin F. Willeke, Jan Lause, Sarah Müller, Paul G. Fahey, Zhiwei Ding, Kelli Restivo, Shashwat Sridhar, Tim Gollisch, Philipp Berens, Andreas S. Tolias, Thomas Euler, Matthias Bethge, Alexander S. Ecker Most discriminative stimuli for functional cell type identification arXiv preprint · system identification · arXiv
Kacper Ksiezak, Rene Burghardt, Neda Shahidi^, Alexander Gail^, Fabian H. Sinz^* Predicting choices in a dyadic foraging task using gated recurrent networks Complex Networks 2023 , equal contribution: ^* extended abstract · system identification ·
Pawel A. Pierzchlewicz, Konstantin F. Willeke, Arne F. Nix, Pavithra Elumalai, Kelli Restivo, Tori Shinn, Cate Nealley, Gabrielle Rodriguez, Saumil Patel, Katrin Franke, Andreas S. Tolias, Fabian H. Sinz Energy Guided Diffusion for Generating Neurally Exciting Images NeurIPS conference paper · system identification · bioRxiv github paper · project page
Konstantin F. Willeke, Paul G. Fahey, Mohammad Bashiri, Laura Hansel, Christoph Blessing, Konstantin-Klemens Lurz, Max F. Burg, Santiago A. Cadena, Zhiwei Ding, Kayla Ponder, Taliah Muhammad, Saumil S. Patel, Kaiwen Deng, Yuanfang Guan, Yiqin Zhu, Kaiwen Xiao, Xiao Han, Simone Azeglio, Ulisse Ferrari, Peter Neri, Olivier Marre, Adrian Hoffmann, Kirill Fedyanin, Kirill Vishniakov, Maxim Panov, Subash Prakash, Kishan Naik, Kantharaju Narayanappa, Alexander S. Ecker, Andreas S. Tolias, Fabian H. Sinz Retrospective on the SENSORIUM 2022 competition Proceedings of Machine Learning Research journal paper · system identification · competition page PMLR pdf
Polina Turishcheva, Paul G. Fahey, Laura Hansel, Rachel Froebe, Kayla Ponder, Michaela Vystrčilová, Konstantin F. Willeke, Mohammad Bashiri, Eric Wang, Zhiwei Ding, Andreas S. Tolias, Fabian H. Sinz, Alexander S. Ecker The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videos arXiv preprint · system identification · arXiv
Konstantin F. Willeke¹, Kelli Restivo¹, Katrin Franke, Arne F. Nix, Santiago A. Cadena, Tori Shinn, Cate Nealley, Gabby Rodriguez, Saumil Patel, Alexander S. Ecker, Fabian H. Sinz², Andreas S. Tolias² Deep learning-driven characterization of single cell tuning in primate visual area V4 unveils topological organization bioRxiv , equal contribution: ¹, ² preprint · system identification · bioRxiv
Konstantin-Klemens Lurz¹, Mohammad Bashiri¹, Edgar Y. Walker, Fabian H. Sinz Bayesian Oracle for bounding information gain in neural encoding models ICLR 2023 , equal contribution: ¹ conference paper · system identification · openreview code video

2022

Erick Cobos, Taliah Muhammad, Paul G Fahey, Zhiwei Ding, Zhuokun Ding, Jacob Reimer, Fabian H. Sinz, Andreas Tolias It takes neurons to understand neurons: Digital twins of visual cortex synthesize neural metamers biorXiv preprint · system identification inception loops · biorXiv
Konstantin Lurz, Mohammad Bashiri, Fabian Sinz Bayesian Oracle for bounding information gain in neural encoding models Neurips 2022 Workshop InfoCog workshop paper · system identification ·
Luca Baroni¹, Mohammad Bashiri¹, Konstantin Friedrich Willeke, Ján Antolík, Fabian Sinz Learning Invariance Manifolds of Visual Sensory Neurons Neurips 2022 Workshop NeurReps , equal contribution: ¹ workshop paper · system identification · PMLR pdf
Konstantin F. Willeke, Paul G. Fahey, Mohammad Bashiri, Laura Pede, Max F. Burg, Christoph Blessing, Santiago A. Cadena, Zhiwei Ding, Konstantin-Klemens Lurz, Kayla Ponder, Taliah Muhammad, Saumil S. Patel, Alexander S. Ecker, Andreas S. Tolias, Fabian H. Sinz The Sensorium competition on predicting large-scale mouse primary visual cortex activity arXiv preprint · system identification · arXiv challenge data

2021

Mohammad Bashiri, Edgar Y. Walker, Konstantin-Klemens Lurz, Akshay Kumar Jagadish, Taliah Muhammad, Zhiwei Ding, Zhuokun Ding, Andreas S. Tolias, Fabian H. Sinz A flow-based latent state generative model of neural population responses to natural images NeurIPS (spotlight) conference paper · system identification · openreview twitter teaser-youtube talk-youtube github simulation demo biorXiv
Max F. Burg, Santiago A. Cadena, George H. Denfield, Edgar Y. Walker, Leon A. Gatys, Andreas S. Tolias, Matthias Bethge, Alexander S. Ecker Learning Divisive Normalization in Primary Visual Cortex PLoS Computational Biology journal paper · system identification normative models · bioRxiv PLoSCB
Konstantin-Klemens Lurz, Mohammad Bashiri, Konstantin Friedrich Willeke, Akshay Kumar Jagadish, Eric Wang, Edgar Y Walker, Santiago Cadena, Taliah Muhammad, Eric Cobos, Andreas Tolias, Alexander Ecker, Fabian Sinz Generalization in data-driven models of primary visual cortex ICLR (spotlight) conference paper · system identification · openreview bioRxiv twitter data code youtube

2020

James R. Cotton, Fabian H. Sinz, Andreas S. Tolias Factorized Neural Processes for Neural Processes: K-Shot Prediction of Neural Responses NeurIPS conference paper · system identification · proceedings arXiv youtube data code
Ivan Ustyuzhaninov, Santiago A. Cadena, Emmanouil Froudarakis, Paul G. Fahey, Edgar Y. Walker, Erick Cobos, Jacob Reimer, Fabian H. Sinz, Andreas S. Tolias, Matthias Bethge, Alexander S. Ecker Rotation-invariant clustering of functional cell types in primary visual cortex ICLR (oral) conference paper · system identification · openreview

2019

Santiago A. Cadena, Fabian H. Sinz, Taliah Muhammad, Emmanouil Froudarakis, Erick Cobos, Edgar Y. Walker, Jake Reimer, Matthias Bethge, Andreas Tolias, Alexander S. Ecker How well do deep neural networks trained on object recognition characterize the mouse visual system? NeurIPS workshop on Real Neurons & Hidden Units (accepted for talk) workshop paper · system identification · openreview
Alexander S. Ecker, Fabian H. Sinz, Emmanouil Froudarakis, Paul G. Fahey, Santiago A. Cadena, Edgar Y. Walker, Erick Cobos, Jacob Reimer, Andreas S. Tolias, Matthias Bethge A rotation-equivariant convolutional neural network model of primary visual cortex ICLR 2019 conference paper · system identification · arXiv openreview code
S. A. Cadena, G. H. Denfield, E. Y. Walker, L. A. Gatys, A. S. Tolias, M. Bethge, and A. S. Ecker Deep convolutional models improve predictions of macaque V1 responses to natural images PLoS Computational Biology journal paper · system identification · PLoS

2018

Fabian H. Sinz, Alexander S. Ecker, Paul G. Fahey, Edgar Y. Walker, Erick Cobos, Emmanouil Froudarakis, Dimitri Yatsenko, Xaq Pitkow, Jacob Reimer, Andreas S. Tolias Stimulus domain transfer in recurrent models for large scale cortical population prediction on video NeurIPS conference paper · system identification · bioRxiv NeurIPS code data